XYLT2 p.Arg243=
c.729C>T · rs1226618202 · VCV3055396
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.005%, amr)
Conditions
1
XYLT2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -14 | GERP -3.1 |
| Overall | ||
| CADD | 2.606 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/60,000 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000668%
Overall
0.000372%
6/1,613,284 alleles · very rare
exomes 5/1,461,042 · genomes 1/152,242 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.005% | 20,000 |
| South Asian | 0.0022% | 45,533 |
| European (non-Finnish) | 8.47e-05% | 1,179,956 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- XYLT2
- Protein
- p.Arg243=
- Coding
- c.729C>T
- MANE Select
- NM_022167
- dbSNP
- rs1226618202
- Type
- single nucleotide variant
- Location
- chr17:50354508 (GRCh38)
- Gene constraint
- LOEUF 0.689 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.79
Disease context
XYLT2-related disorder
Similar variants
- XYLT2 p.Arg243His Uncertain significance ★★ ⚠ same residue
- XYLT2 p.Arg504Trp Uncertain significance ⚠ same condition
- XYLT2 p.Arg730Gln Uncertain significance ⚠ same condition
- XYLT2 p.Arg563Cys Likely pathogenic ★★ same type
- XYLT2 p.Ala254Val Uncertain significance ★★ ⚠ same type
- XYLT2 p.Ala543Thr Uncertain significance ★★ ⚠ same type
- XYLT2 p.Ala570Thr Uncertain significance ★★ ⚠ same type
- XYLT2 p.Ala614Val Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/xylt2-p-arg243 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown